use strict;
use warnings;


my %lista2=
  (
   1    =>    "CAT00.3",
   2    =>    "CAT43.1",
   3    =>    "CAT40.3"
  );

while (<DATA>) {
    s/^>(\d+)/$lista2{$1} || die "unknown number $1"/e;
    print 
}


__DATA__
>1
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>2
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>3
AACTCTGGGACAATGGCACACGGGAAACAGATAATGAACGATCAGCACAGGGAACTAGCG
>4